11-62929479-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_002957251.2(LOC105369333):n.283-73A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,944 control chromosomes in the GnomAD database, including 21,045 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.52 (21045 hom., cov: 32)
• Consequence: LOC105369333 XR_002957251.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

Genes affected

LOC105369333 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369333	XR_002957251.2	n.283-73A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79391 AN: 151826 Hom.: 21012 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.534

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.523 AC: 79471 AN: 151944 Hom.: 21045 Cov.: 32 AF XY: 0.530 AC XY: 39330 AN XY: 74242

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.537

Alfa AF: 0.521 Hom.: 27310

Bravo AF: 0.524

Asia WGS AF: 0.625 AC: 2174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	4.2
Dann	Benign	0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1938677; hg19: chr11-62696951;